Fig. 1

Wnt family evolution in chordates. a The ML phylogenetic tree reveals a conservative pattern of genomic evolution in cephalochordates (species names in blue), which preserve all 13 Wnt subfamilies, contrasting with the dynamic pattern of genomic evolution in urochordates (in red), which are characterized by several gene losses and duplications. The scale bar indicates amino acid substitutions. Values for the approximate likelihood ratio test (aLRT) are shown at nodes. Species are as follows. Chordate species: Urochordates: Botryllus schlosseri (Bsc), Ciona savignyi (Csa), Ciona robusta (Cro; formerly Ciona intestinallis), Halocynthia roretzi (Hro), Halocynthia aurantium (Hau), Mogula occulta (Moccu), Mogula oculata (Mocul), Mogula occidentalis (Mocci), Phallusia fumigata (Pfu), and Phallusia mammillata (Pma). Cephalochordates: Branchiostoma belcheri (Bbe), Branchiostoma floridae (Bfl), Branchiostoma lanceolatum (Bla). Vertebrates: Danio rerio (Dre), Homo sapiens (Hsa). Non-chordates species: hemichordate Saccoglossus kowalevskii (Sko), annelid Capitella teleta (Cte), mollusk Lottia gigantea (Lgi), and cnidarian Nematostella vectensis (Nve). b The Wnt gene catalog (Wnt1–11, Wnt16 and WntA) present (white squares) or absent (red squares) in the three chordate subphyla, allowing inference of plausible events of gene losses (red circles; the number or letter inside the circle indicates the lost Wnt subfamily) and duplications (black squares; the number inside the square indicates the duplicated subfamily) during the evolution of different lineages. While some losses appear to be ancestral (e.g., Wnt8 and Wnt4 losses in stem urochordates), others only affected specific groups or species (e.g., Wnt1 loss in Phlebobranchia, Wnt11 in Molgulas, and Wnt3 in Botryllus). In vertebrates, Wnt subfamilies expanded following the rounds of whole-genome duplications (WGD) that occurred during their early evolution [4], while in the rest of chordates all Wnt are conserved as a single copy, with the exception of Wnt5 in Stolidobranchian ascidians, which has suffered multiple events of tandem gene duplications (see Additional file 1: Figure S1)